One pair of answers is given by the P'rishah, Yoreh Deah 314(14). His second answer is simpler: since the case of the Yisroel is only a safek bechor, there is never more than a safek issur, so Chazal did not need to enforce their suspicion.
His first answer is interesting: We don't actually suspect a Cohen (or a Yisroel) of being willing to violate the Torah (the issur of intentionally making a mum on a korban) just for the benefit of eating it. The real reason the Cohen is suspected is that he is stuck taking care of the animal indefinitely, unless it gets a mum. It's that unbounded obligation that causes the suspicion.
So for our case of safek bechor, that reason doesn't apply. If the Yisroel ever gets too frustrated with waiting, he can just give the animal to a Cohen (and the Shulkhan Arukh poskins that the Cohen has to take it).
This reminds me of another issue: the question of whether a bechor is a positive or a negative - see the question I asked elsewhere (
https://gemaraboards.forumotion.com/t116-bechor-positive-or-negative). Does this answer only make sense if a bechor is a net negative? Or might the owner get desperate anyhow, when it happens that this bechor turns out to be bulletproof for years?
Update 1/21/2017: I have a few other problems with the Prishah's first answer.
1) He rejects that the owner would intentionally make a mum just to be able to eat it. But that seems to be an accepted point of view in the gemara, where a "Ro'eh Cohen" might be a Yisroel shepherd working for a Cohen, hoping to get part of the feast when the bechor is slaughtered. Or a Cohen shepherd working for a Yisroel, who hopes to be given the animal as the designated Cohen when it gets its mum.
2) He is going with his shitah that the Cohen is required to accept the animal from a Yisroel, even if it is a safek bechor. The Rema says that too, I guess that's the halacha, but the poskim bring that other kadmonim (Terumas Hadeshen and others) disagree. If the Cohen doesn't need to accept it, the Yisroel can be desperate on the case of safek bechor as well.
3) If it is allowed to be machnis l'kipah, as some Rishonim hold (but not the Shulchan Aruch), a Cohen wouldn't get desperate either.